ID code consistency between .fam and RRB phenotypes
- The .fam IDs and RRB phenotype IDs are not consistent
- A match list can be found in microarray/Microarray_clean.txt
- Then update RRB phenotypes based on .fam IDs
Structure of three SSC chips
- 10220 Individuals from 2591 SSC families were genotyped on three chips.
- Note that members of each family were analyzed on the same array.
Illumina 1Mv3
- 1189 families
- 4626 people (2703 males, 1923 females)
- 1199033 SNPs
Illumina 1Mv1
- 333 families
- 1354 people (801 males, 553 females)
- 1072814 SNPs
Illumina HumanOmni2.5M
- 1069 families
- 4240 people (2490 males, 1750 females)
- 2440283 SNPs
RRB phenotypes
Phenotype discription
- phenotype counts and levels
- primary and secondary variable information for probands
Probands (2588 individuals)
- 56 phenotypes including age, sex and race
Unaffected Siblings (2098 individuals)
- 27 phenotypes including sex
Other Siblings (296 individuals)
Phenotype distributions
Probands

Unaffected Siblings

Other Siblings

Shared phenotypes
- Proband VS Unaffected Siblings: 15
- Proband VS Other Siblings: 14
- Unaffected Siblings VS Other Siblings: 26
- Proband VS Unaffected Siblings VS Other Siblings: 14
Shared phenotype distribution
Probands VS Unaffected Siblings
***
Probands VS Other Siblings

Probands VS Siblings

Pairwise IBD estimation
- Using plink –genome rel-check based on genome-wide QCd genotypes
- Genotype QC: –geno 0.05 –hwe 1e-6 –mind 0.1 –maf 0.01; further pruned on the SNPs --indep-pairwise to prune in ~50K SNPs
- Only individuals within same family is checked
- Relationships (RT): OT (Parents), FS (Full Siblings), PO (Parent Offspring)
Estimated pairwise IBD distributions
Illumina 1Mv3

Illumina 1Mv1

Illumina Omni2.5

Estimated pairwise IBD VS. Chr-X F
Illumina 1Mv3

Illumina 1Mv1

Illumina Omni2.5

Individual genome-wide heterozygosity
- Using --het to calculate genome-wide (using pruned SNPs) heterozygosity
- Mean heterozygosity = (N-O/N); Het_mean <- (N.NM. - O.HOM.)/N.NM.
- Using --missing to calculate missing rates (individuals with missing rates > 0.1 will be removed)
Genome-wide heterozygosity VS missing rates


- Grey horizontal line is y = mean +/- 3SD
- Red horizontal line is y = mean +/- 5SD
- Grey vertical line is x = 0.1
Genome-wide heterozygosity VS IBD estimation (PI_HAT)
Illumina 1Mv3

Illumina 1Mv1

Illumina Omni2.5
